cell_type_name = "CD8T"
file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 23.00 24.00 25.00 24.55 25.00 26.00
## [1] 40
## [1] 23 23 23 23 23 23 23 23 23 24 24 24 24 24 24 24 24 24 25 25 25 25 25 25 25
## [26] 25 25 25 25 25 25 26 26 26 26 26 26 26 26 26
## [1] 982
bioMart.All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]alias2Symbol function from
limma.a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "C7orf55"
## [1] "FMC1-LUC7L2" "FMC1"
## [1] "MARS"
## [1] "MARS1" "SLA2"
## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "APITD1"
## [1] "CENPS-CORT" "CENPS"
## [1] "HIST1H2BC"
## [1] "H2BC5" "H2BC4"
##
## FALSE TRUE
## 1120 139
##
## FALSE TRUE <NA>
## 71 1049 139
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: ZNRD1 POLR1H
## 2: C2orf43 LDAH
## 3: FAM45A DENND10
## 4: MTERF MTERF1
## 5: NARG2 ICE2
## 6: C6orf203 MTRES1
## 7: HRSP12 RIDA
## 8: FOPNL CEP20
## 9: WARS WARS1
## 10: LINS LINS1
## 11: RRNAD1 METTL25B
## 12: FAM122B PABIR2
## 13: WDYHV1 NTAQ1
## 14: HIST1H2BD H2BC5
## 15: AGPAT6 GPAT4
## 16: C1orf123 CZIB
## 17: KIAA1841 SANBR
## 18: C2orf44 WDCP
## 19: TMEM155 SMIM43
## 20: C7orf55 FMC1-LUC7L2
## 21: C9orf89 CARD19
## 22: C11orf82 DDIAS
## 23: XRCC6BP1 ATP23
## 24: MARS MARS1
## 25: C19orf55 PROSER3
## 26: HIST1H2AE H2AC8
## 27: QARS EPRS1
## 28: APITD1 CENPS-CORT
## 29: CCDC101 SGF29
## 30: PDDC1 GATD1
## 31: EFCAB4A CRACR2B
## 32: EIF2S3L EIF2S3B
## 33: HIST1H2BC H2BC5
## 34: WRB GET1
## 35: TMEM194B NEMP2
## 36: HIST1H4C H4C3
## 37: HIST1H4J H4C11
## 38: ZNF720 KRBOX5
## 39: HIST1H2BH H2BC9
## 40: FAM49A CYRIA
## 41: TTC37 SKIC3
## 42: C1orf85 GLMP
## 43: C9orf114 SPOUT1
## 44: HIST2H2AA4 H2AC19
## 45: HIST2H2BF H2BC18
## 46: C10orf128 TMEM273
## 47: TCTEX1D2 DYNLT2B
## 48: C17orf89 NDUFAF8
## 49: PHBP3 PHB1P3
## 50: SEPT7P7 SEPTIN7P7
## 51: LINC00493 SMIM26
## 52: HIST1H2BN H2BC15
## 53: ATP5J2 ATP5MF
## 54: AKAP2 PALM2AKAP2
## 55: WDR65 CFAP57
## 56: SRP14-AS1 SRP14-DT
## 57: CTC-436P18.1 SMIM15-AS1
## 58: HIST1H3G H3C8
## 59: EFTUD1P1 EFL1P1
## 60: ATP5A1P3 ATP5F1AP3
## 61: CCDC109B MCUB
## 62: C1orf63 RSRP1
## 63: TMEM66 SARAF
## 64: PCNXL2 PCNX2
## 65: ACRC GCNA
## 66: AMICA1 JAML
## 67: PRMT10 PRMT9
## 68: FAM102A EEIG1
## 69: SELM SELENOM
## 70: NBPF16 NBPF15
## 71: RPL9P9 RPL9P8
## sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma), gene_symbol := sym_limma]
dim(gene_info)## [1] 1259 3
## sym_in_data sym_limma gene_symbol
## 1: C1orf112 C1orf112 C1orf112
## 2: MAD1L1 MAD1L1 MAD1L1
## 3: ICA1 ICA1 ICA1
## 4: NDUFAF7 NDUFAF7 NDUFAF7
## 5: ST7 ST7 ST7
## t1
## 1 2
## 1255 2
## sym_in_data sym_limma gene_symbol
## 1: HIST1H2BD H2BC5 H2BC5
## 2: HIST1H2BC H2BC5 H2BC5
## 3: RPL9P8 RPL9P8 RPL9P8
## 4: RPL9P9 RPL9P8 RPL9P8
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
gmtfile[["immune"]] = "../Annotation/c7.all.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp" "immune"
## reactome go_bp immune
## 1692 7647 5219
Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
##
## $immune
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5 162 193 197 199 199 200 200 200 200 1992
## [1] 1259 3
## sym_in_data sym_limma gene_symbol
## 1: C1orf112 C1orf112 C1orf112
## 2: MAD1L1 MAD1L1 MAD1L1
max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol")
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=120)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "MTIF2" "KHSRP" "MRPS33" "NDUFAF5" "CDK5RAP1" "EARS2"
## [7] "MTFMT" "SARS2" "GTPBP10" "DHX58" "ATPAF1" "NDUFAF4"
## [13] "C6orf203" "MTO1" "MRRF" "MALSU1" "MRPL55" "NDUFS4"
## [19] "PHAX" "MRPL48" "ZNF431" "MRPL23" "CCDC109B"
## [1] 2
## [1] "CENPQ" "CENPO" "ZNF816" "RPS17" "TNF" "APBA2" "RPL34"
## [8] "RPS12" "RASGRF2" "EGR1" "RPL21" "FOSB" "JUND" "SORL1"
## [15] "RPS27A" "RPL9" "RBKS" "JUNB" "RPLP2" "RPS27" "DNHD1"
## [22] "RPS23" "RPS18"
## [1] 3
## [1] "MAD1L1" "SLC25A14" "ERCC2" "IMPDH1" "C17orf75" "GTF2H3"
## [7] "CDC20" "DCAF4" "CKS2" "MCEE" "UROD" "PDZD2"
## [13] "CCNB1" "CDK7" "COPS3" "CCNB2" "MTHFD2L" "POLE"
## [19] "BTLA" "HIST1H4J" "PRIM1" "C1orf85" "STK19" "MUC20"
## [1] 4
## [1] "DERL2" "SMUG1" "GLUL" "TMOD3" "LINS" "PLIN2"
## [7] "MZT2B" "HIST1H2BD" "GLB1" "KBTBD2" "IFRD2" "C17orf89"
## [13] "PPIL3" "IFRD1" "PIK3IP1" "YPEL5" "BTG1" "SLC38A2"
## [19] "SKIL" "PDCD4" "FAM102A" "PFKFB3" "RALGAPA1"
## [1] 5
## [1] "TBPL1" "NT5C2" "WDR13" "IFI6"
## [5] "XAF1" "TMEM241" "APH1B" "WARS"
## [9] "GTF2A2" "TATDN1" "LZTFL1" "TRIM68"
## [13] "GTSF1" "FCRL6" "PSMG1" "UBXN2B"
## [17] "TSTD1" "TRGC2" "PATL2" "TRGV2"
## [21] "AC092580.4" "RP11-552M11.4" "HMGB1P24" "AC139149.1"
## [25] "CTD-3214H19.4"
## [1] 6
## [1] "MFAP3" "FAR2" "CAPN15" "PIEZO1" "POP4" "CD86"
## [7] "CD160" "DHDDS" "NPC2" "IFIT3" "IFIT2" "NME2P1"
## [13] "L3HYPDH" "HRSP12" "PRMT7" "DPH6" "C1orf123" "CTLA4"
## [19] "POP5" "IFIT1" "TMEM120A" "POTEKP" "PVT1"
## [1] 7
## [1] "KHDC1" "ABHD16B" "ZNF93" "NPM1P33"
## [5] "RP11-247I13.3" "RP11-270C12.3" "PGAM4" "PIN4P1"
## [9] "RP11-247I13.6" "SEPT7P7" "PA2G4P4" "RP11-782C8.1"
## [13] "BTF3P10" "RPS27AP2" "AC007041.2" "RPS19P3"
## [17] "RN7SL56P" "GAPDHP60" "RNF138P1" "KB-1507C5.2"
## [21] "SLC2A3P4" "HSPA8P5" "ANP32AP1" "CTB-52I2.4"
## [25] "CTD-2545M3.2" "RP4-739H11.4"
## [1] 8
## [1] "MAP4K5" "KIF4A" "SPTLC2" "RAD51C"
## [5] "MCM9" "SMC4" "CACYBP" "AKR1A1"
## [9] "CCR2" "TEP1" "NPHP4" "SLC2A8"
## [13] "HIRIP3" "RNF207" "LRRC28" "PLA2G6"
## [17] "EFCAB7" "HSPA1B" "TRAV21" "NAP1L1P3"
## [21] "RP11-773D16.1" "RP11-307P22.1" "CTD-2521M24.9" "C1orf63"
## [25] "RP11-727F15.9"
## [1] 9
## [1] "VPS41" "SH3BP2" "DEPDC5" "ARHGEF18" "LIG1" "DDX49"
## [7] "BRD8" "NPRL2" "CHTF18" "TPGS2" "ACTL6A" "MTF2"
## [13] "SUV39H2" "FARP1" "CXXC1" "TAF10" "TRAPPC11" "RMDN1"
## [19] "TECPR1" "SSH2" "PIP4K2A" "BRD2" "PPP1R10"
## [1] 10
## [1] "PTPN18" "MAP3K13" "ZNF684" "TXNDC17"
## [5] "PUS7L" "TROAP" "GEMIN6" "MPPE1"
## [9] "KIAA1841" "CTSB" "C11orf82" "TBCA"
## [13] "ZBED2" "GEN1" "TMEM194B" "RP11-64B16.2"
## [17] "NCKIPSD" "AC098614.2" "RPF2P1" "CCT8P1"
## [21] "BDH2P1" "GAPDHP2" "RP11-844P9.3" "PAICSP4"
## [25] "RP11-473N11.2"
## [1] 11
## [1] "CD84" "ZNF85" "GALK1" "MS4A6A"
## [5] "STK25" "CCRL2" "STYXL1" "NARG2"
## [9] "TMEM138" "ZBTB39" "ZNF613" "SPATA13"
## [13] "CCDC30" "RP11-12M9.4" "HNRNPKP2" "RP3-342P20.2"
## [17] "PA2G4P2" "AC002331.1" "HNRNPA1P55" "CCL3L3"
## [21] "RBBP4P5" "HMGB1P8" "HNRNPA1P16" "CTB-31O20.3"
## [25] "RP11-686D22.10"
## [1] 12
## [1] "TM7SF3" "TIPIN" "TIMM9" "PLA2G15" "GABPB1"
## [6] "DOT1L" "ZNF419" "DUS4L" "LOXL3" "FANCL"
## [11] "TIMM10" "RNF121" "CCDC28B" "RNF25" "PRIMPOL"
## [16] "CDCA7L" "SESTD1" "TDRD7" "GM2A" "CHAMP1"
## [21] "FANCG" "GK3P" "RP11-402J6.3" "ATP5A1P3"
## [1] 13
## [1] "PIM2" "HAVCR1" "PECR" "USF1" "FCRL3"
## [6] "WDR41" "NAALADL1" "AC004840.9" "COA3" "CMC1"
## [11] "CCL3L1" "RAB12" "TRAV24" "RP11-2F9.3" "MIR29B1"
## [16] "PET100" "RP11-693N9.2" "LINC00426" "RN7SL749P" "AC005329.7"
## [21] "AP000462.1" "SNORD3A" "C9orf72" "MS4A1"
## [1] 14
## [1] "DYRK4" "GLT8D1" "ID3" "MFSD9"
## [5] "TMEM19" "NTAN1" "TMSB15B" "ZNF511"
## [9] "RP13-383K5.4" "CD27-AS1" "UBA52P6" "ACTBP8"
## [13] "RPL19P12" "ARPC3P1" "PHBP3" "ATF4P3"
## [17] "TCP1P1" "TPI1P2" "ETF1P2" "RPL13P5"
## [21] "RPL37P23" "GAPDHP38" "RP11-382J24.2" "PSMC1P9"
## [25] "MIR3661" "AC024592.12"
## [1] 15
## [1] "NOP16" "NTHL1" "WDR7" "THOC5" "FAHD2A"
## [6] "NENF" "METTL8" "EMG1" "IMP4" "C19orf47"
## [11] "WDR43" "ZFP62" "ZNF770" "ZBTB48" "UAP1"
## [16] "SGSM2" "RPL32" "EPB41" "CXCR5" "ZNF589"
## [21] "RPS26" "SELM" "RP11-51J9.5"
## [1] 16
## [1] "REC8" "DHRS12" "GDAP1" "PRR4"
## [5] "SCPEP1" "ORMDL2" "RRM2" "MZT2A"
## [9] "ASB8" "HIST1H4C" "SLC26A6" "RP11-386G11.10"
## [13] "RGCC" "CPQ" "FOXP1" "PMEPA1"
## [17] "FAM117B" "NPAT" "TC2N" "GPR183"
## [21] "PLK3" "GOLGA8A" "SATB1" "TSC22D2"
## [1] 17
## [1] "NDUFAF7" "NSMAF" "IL4R" "USP48" "UTP6" "PTP4A1" "MYB"
## [8] "PGPEP1" "PPCDC" "NARF" "PMAIP1" "PPOX" "SEC24D" "FCGR3B"
## [15] "FBXO22" "ZNF232" "GNG4" "BOLA1" "CAPN12" "FCGR3A" "LEF1"
## [22] "GNAQ" "DHRS3" "NR1D2"
## [1] 18
## [1] "DUSP12" "AAAS" "DHPS" "NUP107" "GALE" "NUP85"
## [7] "COQ3" "FHOD1" "ASNSD1" "UCK2" "LPP" "CETN3"
## [13] "VPS37A" "GALK2" "AGPAT6" "NFU1" "TMEM126A" "CTDNEP1"
## [19] "UCKL1" "ATP5J2" "ABHD14A" "GGT7" "OBSCN"
## [1] 19
## [1] "RP3-324O17.4" "MDGA1" "PDE6B" "SLC35A5"
## [5] "GSTM4" "LRTOMT" "MYL5" "XXbac-B562F10.11"
## [9] "GS1-124K5.2" "GYG1P3" "AC115617.2" "GOT2P3"
## [13] "CTD-2301A4.3" "ACRC" "POU6F1" "TCEAL3"
## [17] "RP11-91K8.4" "ACTBP12" "RP1-187B23.1" "AP001468.1"
## [21] "ATP1B3-AS1" "RP11-44N11.1" "TMEM9B-AS1" "LINC00944"
## [25] "RP11-320M16.1" "CTD-2017D11.1"
## [1] 20
## [1] "TMEM134" "ZBTB8OS" "C2orf76" "RPSAP47"
## [5] "ZNF28" "TRGV10" "RPSAP54" "RP4-694B14.5"
## [9] "KANSL1-AS1" "RNU2-63P" "NPM1P19" "RP11-350G8.3"
## [13] "SAPCD1" "RP11-567G24.1" "AC093391.2" "EEF1A1P14"
## [17] "CDC42P1" "FAM200B" "AC018462.3" "EEF1A1P10"
## [21] "CTB-33G10.1" "TPM3P6" "RP11-1012A1.7" "RP13-638C3.4"
## [25] "RP11-209D14.4" "ACTBP9"
## [1] 21
## [1] "ICA1" "GBA2" "REXO1" "RABGGTA" "ILVBL"
## [6] "SRM" "PARP2" "FGFBP2" "MMS22L" "SPON2"
## [11] "COG5" "XRCC6BP1" "NT5DC1" "HIST1H2BC" "ZNF765"
## [16] "HIST2H2AA4" "HIST2H2BF" "TRAV14DV4" "LINC00493" "CNOT7P1"
## [21] "HIST1H2BN" "AC004069.2" "HIST1H3G" "HNRNPA1P50" "FRMD4A"
## [1] 22
## [1] "C1orf112" "AGA" "RNF13" "P2RX5" "GSR" "TYK2"
## [7] "GOSR2" "FIGNL1" "IDH1" "TAMM41" "TOMM40L" "B2M"
## [13] "AFMID" "KNTC1" "ENTPD5" "TMSB4X" "TREX1" "RGPD5"
## [19] "DKK3" "PPP2R5C" "STK17B" "EPHA1" "NELL2" "MALAT1"
## [1] 23
## [1] "ZNF268" "RRNAD1" "THAP2" "SNHG11"
## [5] "EIF2S3L" "CATSPER2P1" "TRAV35" "RP11-383G10.3"
## [9] "CALM2P3" "RPS12P26" "AC090804.1" "SKP1P1"
## [13] "RPS11P5" "CTC-338M12.4" "MAPKAPK5-AS1" "RP11-446E9.1"
## [17] "RP11-32B5.1" "AP000476.1" "FAM21FP" "RP11-394D2.1"
## [21] "RBBP4P1" "RP11-638I2.10" "CTD-2022H16.3" "RP11-304L19.5"
## [25] "RP11-265N6.3" "AC006129.4"
## [1] 24
## [1] "MED24" "ZNRD1" "POLR2I" "NSMCE4A"
## [5] "EPAS1" "UXT" "SLC41A2" "CLSTN3"
## [9] "TBCD" "MFSD6" "PPP4R1" "ALG8"
## [13] "MED11" "POLR2H" "IL15" "MEI1"
## [17] "LCORL" "TMEM107" "PPARA" "TRGV3"
## [21] "MRPL33" "RP11-33B1.1" "RP11-416A17.6" "MIR3615"
## [25] "RP11-297D21.4"
## [1] 25
## [1] "MTHFS" "DRAM2" "RHEBL1" "LRRC45"
## [5] "NME6" "PIGW" "MT1X" "ZNF720"
## [9] "TRBV4-2" "TRAV19" "ANAPC10P1" "RSC1A1"
## [13] "RP11-122G18.7" "RP11-350G13.1" "RP11-119F19.2" "NPM1P34"
## [17] "AC104820.2" "RP11-262H14.3" "NDUFA9P1" "RPSAP4"
## [21] "WDR65" "RP11-179A18.1" "TRGV7" "CTB-4E7.1"
## [25] "AL161784.1" "RP11-705C15.5"
## [1] 26
## [1] "TNFRSF9" "EVC" "NFE2L1" "CRTAM"
## [5] "C3orf14" "SMIM19" "RP11-254B13.4" "BACH2"
## [9] "NBPF14" "NR4A2" "AMICA1" "NBPF10"
## [13] "AC018720.10" "NAA16" "CHD2" "TSHZ2"
## [17] "TTC3" "PLGLB1" "KLHL25" "NBPF16"
## [21] "AC084018.1" "HCG4P5" "MTND4P12" "RP11-335G20.7"
## [25] "SLC7A5P1"
## [1] 27
## [1] "MBNL3" "FAH" "SNX8" "SCRN2"
## [5] "FUOM" "OXSM" "FAM122B" "DBF4B"
## [9] "DNASE1" "RP3-395M20.8" "DBNDD2" "AP000620.1"
## [13] "TPMTP1" "PLXND1" "AOAH" "CDC42EP3"
## [17] "ZMAT1" "RPS3AP26" "RP11-572P18.1" "RPL10P3"
## [21] "RPL9P8" "RPL3P4" "RPS3AP6" "RPL9P9"
## [25] "RPL9P7"
## [1] 28
## [1] "EGR2" "IL10" "TNFAIP8L2" "C19orf55"
## [5] "CMAHP" "ARHGAP11B" "ZNF257" "AC018804.7"
## [9] "AC009403.2" "LYPLA1P3" "AC012318.3" "RP4-742C19.12"
## [13] "ZNF826P" "AC011747.4" "ZEB1-AS1" "RP11-271C24.3"
## [17] "SRP14-AS1" "GMPSP1" "RP11-889L3.4" "MIR146A"
## [21] "SF3A3P2" "USP30-AS1" "TRAV30" "EFTUD1P1"
## [25] "RP11-265N6.2" "RIMKLB"
## [1] 29
## [1] "RNF10" "SMG6" "MICALL1" "GMPR2" "CNOT2" "MTFR1L"
## [7] "APTX" "CASP1" "HAUS2" "KSR1" "MAP3K6" "LIMD1"
## [13] "C2orf44" "DALRD3" "PCGF5" "CNOT10" "EIF4ENIF1" "ZNF544"
## [19] "TNRC6C" "TNRC6B" "CNOT6L" "BTG2" "PLA2G4B"
## [1] 30
## [1] "CHI3L2" "OCEL1" "NHP2P1" "IL18RAP"
## [5] "C2orf43" "FAM45A" "MTERF" "DTD2"
## [9] "NUDT7" "C9orf89" "ADCK5" "EFCAB4A"
## [13] "SLC9A9" "ZNF525" "TRGV5" "TRBV9"
## [17] "TRDV1" "TRDC" "RP4-800M22.1" "RPL19P21"
## [21] "ADH5P4" "AC144530.1" "STARD4-AS1" "RP11-317N8.4"
## [25] "RP11-1094M14.7" "RP11-282O18.6"
## [1] 31
## [1] "Z97634.3" "RASGRP2" "TCF7" "MAN1C1"
## [5] "ACVR2A" "CCR7" "C1orf162" "PLAC8"
## [9] "LDLRAP1" "PLXDC1" "TMEM150A" "CD248"
## [13] "YPEL2" "TRABD2A" "MIR4461" "CTD-3092A11.1"
## [17] "RP11-632K20.7" "LTB" "CHRM3-AS2" "WHAMMP2"
## [21] "RP11-747H7.3" "RP11-1000B6.3" "KCNQ1OT1" "RP1-313I6.12"
## [25] "RP11-434H6.7"
## [1] 32
## [1] "CCL3" "RABGAP1" "GNPTAB" "SLC12A4" "CCL4" "GCHFR"
## [7] "PRSS23" "TMPRSS3" "SLC39A13" "DNAJC18" "ETFDH" "METTL18"
## [13] "ZNF80" "PDDC1" "WRB" "TNFRSF18" "CCL4L2" "AGER"
## [19] "MSH5" "UBE2D3P2" "MIR142" "PHLDB3" "PER1" "CD55"
## [1] 33
## [1] "CD200" "C14orf93" "TFDP2" "YIPF2"
## [5] "NDUFAF6" "PAQR4" "TMEM155" "LAIR2"
## [9] "TRANK1" "ZNF678" "EDARADD" "CRYGS"
## [13] "LINC00484" "BHLHE40-AS1" "RP11-305L7.3" "RP4-728D4.2"
## [17] "TRAV1-2" "RP11-493L12.6" "PMF1-BGLAP" "DGKA"
## [21] "MAK" "RP11-514P8.6" "RPS26P6" "HLA-W"
## [25] "RP13-488H8.1"
## [1] 34
## [1] "POLD3" "PTPN4" "UBXN8" "IFNG" "RCOR3" "NR2C1" "SNX14"
## [8] "GPN2" "FAM50B" "MITD1" "PPP1R32" "C7orf55" "ATPAF2" "CADM1"
## [15] "SCML1" "TXK" "CLDND1" "ABLIM1" "SLC38A1" "NEK1" "FBXO32"
## [22] "POLR2J3" "LDOC1" "HLA-J"
## [1] 35
## [1] "IFI27" "WDR53" "ZNF749" "FAM49A"
## [5] "ZNF649" "CPT1B" "TRAV8-2" "TRAV13-1"
## [9] "TRAV16" "TRAV29DV5" "PDCL3P5" "NPM1P32"
## [13] "RP1-102E24.1" "RPS19P1" "PSMA6P1" "PTGES3P2"
## [17] "RP3-340B19.5" "PRDX3P1" "RP11-288E14.2" "RPL7AP31"
## [21] "RP11-81H14.2" "MTRNR2L3" "RP11-511H9.4" "RPPH1"
## [25] "AC006483.1" "LUZP6"
## [1] 36
## [1] "CDKL1" "TTLL4" "MGAT4A" "HECA" "RCAN3"
## [6] "NR4A3" "PCNXL2" "RASGEF1B" "TIPARP" "PRMT10"
## [11] "FILIP1L" "ZBTB20" "RGPD6" "DENND5A" "ANKRD37"
## [16] "SELL" "FAM169A" "AC021593.1" "MTND1P23" "LINC00674"
## [21] "PSMD6-AS2" "RP11-285F7.2" "ZNF10" "QRSL1P3"
## [1] 37
## [1] "GCFC2" "OAS1" "GZMB" "ENO3"
## [5] "NCOA7" "GBP1" "MT2A" "RSAD2"
## [9] "SPPL2A" "IRF8" "SFR1" "SLAMF8"
## [13] "AMDHD2" "GNGT2" "KIR3DL1" "ITGAM"
## [17] "NINJ2" "SWI5" "PRF1" "RP11-365H23.1"
## [21] "KIR2DS4" "PTGES3P1" "AKAP2" "KIR2DL3"
## [25] "SERHL2"
## [1] 38
## [1] "PAFAH1B1" "LIN7B" "PON2" "KLRB1" "CCDC77"
## [6] "ACTR10" "FOPNL" "KLRC1" "AHI1" "BORA"
## [11] "CXCL13" "PANK4" "MGAT4B" "SLC38A9" "CEP57L1"
## [16] "HLA-DQA1" "CCL4L1" "KLRC2" "METTL6" "TCTEX1D2"
## [21] "KIR3DL2" "RP11-345J4.6" "MPP7"
## [1] 39
## [1] "TNFSF10" "PTGER2" "IFI44L" "IFI44" "XCL1"
## [6] "XCL2" "TRPT1" "CX3CR1" "MT1E" "HOPX"
## [11] "RP11-23P13.6" "ZNF683" "NAP1L4P1" "MTHFD2P7" "EEF1GP1"
## [16] "C10orf128" "TRBV20-1" "RP5-1053E7.3" "RP1-182O16.1" "RNU2-2P"
## [21] "TSEN15P1" "SNRPEP4" "MIR155HG" "RNU1-125P" "AL358333.1"
## [1] 40
## [1] "EVI5" "WIPI1" "LTBP4" "RGS1"
## [5] "PMM1" "FADS2" "IRF4" "BCAS3"
## [9] "PELP1" "AMFR" "CXCR6" "TRAV12-2"
## [13] "TMEM66" "ATXN7" "NPIPB3" "EIF1"
## [17] "NPIPB4" "GPRASP1" "KLRK1" "MTND2P28"
## [21] "CTD-2328D6.1" "RPL41" "NPIPB5" "MTATP6P1"
## [25] "CTD-2031P19.4"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_1"
## [1] "MTIF2" "KHSRP" "MRPS33" "NDUFAF5" "CDK5RAP1" "EARS2"
## [7] "MTFMT" "SARS2" "GTPBP10" "DHX58" "ATPAF1" "NDUFAF4"
## [13] "C6orf203" "MTO1" "MRRF" "MALSU1" "MRPL55" "NDUFS4"
## [19] "PHAX" "MRPL48" "ZNF431" "MRPL23" "CCDC109B"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 495 mitochondrial translation 2.012426e-10 1.0000000
## 986 translation 1.162489e-06 0.9999999
## numDEInCat numInCat FDR
## 495 7 9 2.056700e-07
## 986 9 46 5.940318e-04
##
## $go_bp
## category over_represented_pvalue
## 1301 mitochondrial gene expression 0.000000e+00
## 1311 mitochondrial translation 0.000000e+00
## 1307 mitochondrial rna metabolic process 2.723763e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 1301 1 11 16 0.0000000000
## 1311 1 9 13 0.0000000000
## 1307 1 5 7 0.0003710674
##
## [1] "set_2"
## [1] "CENPQ" "CENPO" "ZNF816" "RPS17" "TNF" "APBA2" "RPL34"
## [8] "RPS12" "RASGRF2" "EGR1" "RPL21" "FOSB" "JUND" "SORL1"
## [15] "RPS27A" "RPL9" "RBKS" "JUNB" "RPLP2" "RPS27" "DNHD1"
## [22] "RPS23" "RPS18"
## $reactome
## category
## 890 srp dependent cotranslational protein targeting to membrane
## 256 eukaryotic translation initiation
## 734 response of eif2ak4 gcn2 to amino acid deficiency
## 255 eukaryotic translation elongation
## 691 regulation of expression of slits and robos
## 547 nonsense mediated decay nmd
## 808 selenoamino acid metabolism
## 117 cellular response to starvation
## 869 signaling by robo receptors
## 387 influenza infection
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 890 1.367410e-08 1 10 29
## 256 1.878780e-08 1 10 30
## 734 1.912613e-08 1 10 30
## 255 2.552031e-08 1 10 31
## 691 2.648305e-08 1 10 31
## 547 2.815049e-08 1 10 31
## 808 3.633881e-08 1 10 32
## 117 4.808493e-08 1 10 33
## 869 4.815877e-08 1 10 33
## 387 1.736204e-07 1 10 37
## FDR
## 890 4.794966e-06
## 256 4.794966e-06
## 734 4.794966e-06
## 255 4.794966e-06
## 691 4.794966e-06
## 547 4.794966e-06
## 808 5.305467e-06
## 117 5.468696e-06
## 869 5.468696e-06
## 387 1.774400e-05
##
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 515 cytoplasmic translation 3.832737e-09 1.0000000
## 3637 response to salt 2.992022e-06 0.9999999
## 403 cellular response to salt 1.000833e-05 0.9999999
## numDEInCat numInCat FDR
## 515 10 33 0.0000156644
## 3637 5 11 0.0061141980
## 403 4 7 0.0136346749
##
## $immune
## category
## 2358 gse26156 double positive vs cd4 single positive thymocyte up
## 1944 gse22886 naive bcell vs neutrophil up
## 1974 gse22886 naive tcell vs dc up
## 1940 gse22886 naive bcell vs dc up
## 4064 gse42088 uninf vs leishmania inf dc 2h dn
## 1725 gse21670 untreated vs tgfb il6 treated cd4 tcell dn
## 54 gaucher pbmc yf vax stamaril unknown age 7dy dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2358 6.228214e-07 1.0000000 8 36
## 1944 9.271724e-07 1.0000000 7 25
## 1974 7.059308e-06 0.9999996 7 33
## 1940 2.645149e-05 0.9999985 6 28
## 4064 3.236369e-05 0.9999980 6 29
## 1725 3.569177e-05 0.9999985 5 17
## 54 6.796412e-05 0.9999952 6 32
## FDR
## 2358 0.002363826
## 1944 0.002363826
## 1974 0.011998471
## 1940 0.030332052
## 4064 0.030332052
## 1725 0.030332052
## 54 0.049507010
##
## [1] "set_3"
## [1] "MAD1L1" "SLC25A14" "ERCC2" "IMPDH1" "C17orf75" "GTF2H3"
## [7] "CDC20" "DCAF4" "CKS2" "MCEE" "UROD" "PDZD2"
## [13] "CCNB1" "CDK7" "COPS3" "CCNB2" "MTHFD2L" "POLE"
## [19] "BTLA" "HIST1H4J" "PRIM1" "C1orf85" "STK19" "MUC20"
## $reactome
## category
## 326 global genome nucleotide excision repair gg ner
## 967 transcription coupled nucleotide excision repair tc ner
## 574 nucleotide excision repair
## 284 formation of tc ner pre incision complex
## 158 cyclin a b1 b2 associated events during g2 m transition
## 766 rna polymerase i transcription initiation
## 767 rna polymerase i transcription termination
## 283 formation of rna pol ii elongation complex
## 286 formation of the early elongation complex
## 370 hiv transcription elongation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 326 3.628575e-05 0.9999986 5 14
## 967 3.695727e-05 0.9999986 5 14
## 574 1.082683e-04 0.9999945 5 17
## 284 1.614574e-04 0.9999948 4 10
## 158 2.907588e-04 0.9999959 3 5
## 766 2.937602e-04 0.9999958 3 5
## 767 2.937602e-04 0.9999958 3 5
## 283 2.964478e-04 0.9999958 3 5
## 286 2.964478e-04 0.9999958 3 5
## 370 2.964478e-04 0.9999958 3 5
## FDR
## 326 0.01888517
## 967 0.01888517
## 574 0.02754269
## 284 0.02754269
## 158 0.02754269
## 766 0.02754269
## 767 0.02754269
## 283 0.02754269
## 286 0.02754269
## 370 0.02754269
##
## $go_bp
## category over_represented_pvalue
## 1318 mitotic cell cycle phase transition 5.518124e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 1318 0.9999996 8 42 0.02255257
##
## [1] "set_18"
## [1] "DUSP12" "AAAS" "DHPS" "NUP107" "GALE" "NUP85"
## [7] "COQ3" "FHOD1" "ASNSD1" "UCK2" "LPP" "CETN3"
## [13] "VPS37A" "GALK2" "AGPAT6" "NFU1" "TMEM126A" "CTDNEP1"
## [19] "UCKL1" "ATP5J2" "ABHD14A" "GGT7" "OBSCN"
## $reactome
## category
## 562 nuclear envelope breakdown
## 400 interactions of rev with host cellular proteins
## 401 interactions of vpr with host cellular proteins
## 567 nuclear import of rev protein
## 694 regulation of glucokinase by glucokinase regulatory protein
## 904 sumoylation of sumoylation proteins
## 906 sumoylation of ubiquitinylation proteins
## 257 export of viral ribonucleoproteins from nucleus
## 901 sumoylation of dna replication proteins
## 903 sumoylation of rna binding proteins
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 562 2.461663e-05 0.9999996 4 9
## 400 4.158902e-05 0.9999998 3 4
## 401 4.158902e-05 0.9999998 3 4
## 567 4.158902e-05 0.9999998 3 4
## 694 4.158902e-05 0.9999998 3 4
## 904 4.158902e-05 0.9999998 3 4
## 906 4.158902e-05 0.9999998 3 4
## 257 9.827123e-05 0.9999991 3 5
## 901 1.066252e-04 0.9999990 3 5
## 903 1.067353e-04 0.9999990 3 5
## FDR
## 562 0.006071997
## 400 0.006071997
## 401 0.006071997
## 567 0.006071997
## 694 0.006071997
## 904 0.006071997
## 906 0.006071997
## 257 0.010005313
## 901 0.010005313
## 903 0.010005313
##
## [1] "set_21"
## [1] "ICA1" "GBA2" "REXO1" "RABGGTA" "ILVBL"
## [6] "SRM" "PARP2" "FGFBP2" "MMS22L" "SPON2"
## [11] "COG5" "XRCC6BP1" "NT5DC1" "HIST1H2BC" "ZNF765"
## [16] "HIST2H2AA4" "HIST2H2BF" "TRAV14DV4" "LINC00493" "CNOT7P1"
## [21] "HIST1H2BN" "AC004069.2" "HIST1H3G" "HNRNPA1P50" "FRMD4A"
## $reactome
## category
## 356 hdacs deacetylate histones
## 355 hcmv late events
## 352 hats acetylate histones
## 353 hcmv early events
## 354 hcmv infection
## 10 activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 63 assembly of the orc complex at the origin of replication
## 122 chromatin modifications during the maternal to zygotic transition mzt
## 209 dna methylation
## 249 ercc6 csb and ehmt2 g9a positively regulate rrna expression
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 356 1.991681e-05 0.9999995 5 11
## 355 5.548716e-05 0.9999980 5 15
## 352 7.931066e-05 0.9999968 5 16
## 353 9.596559e-05 0.9999959 5 17
## 354 1.234231e-04 0.9999944 5 18
## 10 2.169060e-04 0.9999935 4 9
## 63 2.169060e-04 0.9999935 4 9
## 122 2.169060e-04 0.9999935 4 9
## 209 2.169060e-04 0.9999935 4 9
## 249 2.169060e-04 0.9999935 4 9
## FDR
## 356 0.01847316
## 355 0.01847316
## 352 0.01847316
## 353 0.01847316
## 354 0.01847316
## 10 0.01847316
## 63 0.01847316
## 122 0.01847316
## 209 0.01847316
## 249 0.01847316
##
## [1] "set_29"
## [1] "RNF10" "SMG6" "MICALL1" "GMPR2" "CNOT2" "MTFR1L"
## [7] "APTX" "CASP1" "HAUS2" "KSR1" "MAP3K6" "LIMD1"
## [13] "C2orf44" "DALRD3" "PCGF5" "CNOT10" "EIF4ENIF1" "ZNF544"
## [19] "TNRC6C" "TNRC6B" "CNOT6L" "BTG2" "PLA2G4B"
## $reactome
## category
## 952 tp53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain
## 981 transcriptional regulation by tp53
## 954 tp53 regulates transcription of cell cycle genes
## 172 deadenylation of mrna
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 952 3.560203e-06 1.0000000 4 6
## 981 7.267698e-06 0.9999996 7 35
## 954 1.346275e-05 0.9999998 4 8
## 172 6.478048e-05 0.9999996 3 4
## FDR
## 952 0.003638527
## 981 0.003713794
## 954 0.004586311
## 172 0.016551413
##
## $go_bp
## category
## 1917 nuclear transcribed mrna poly a tail shortening
## 1913 nuclear transcribed mrna catabolic process deadenylation dependent decay
## 1912 nuclear transcribed mrna catabolic process
## 3702 rna destabilization
## 2380 positive regulation of mrna metabolic process
## 3201 regulation of mrna catabolic process
## 1372 mrna catabolic process
## 1456 negative regulation of amide metabolic process
## 3202 regulation of mrna metabolic process
## 3700 rna catabolic process
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1917 3.599968e-11 1.0000000 7 8
## 1913 6.556969e-10 1.0000000 7 10
## 1912 9.780452e-10 1.0000000 8 15
## 3702 1.149893e-08 1.0000000 7 14
## 2380 4.080189e-08 1.0000000 7 16
## 3201 8.518372e-08 1.0000000 7 17
## 1372 9.073724e-08 1.0000000 8 24
## 1456 1.605856e-07 1.0000000 8 29
## 3202 4.392593e-07 1.0000000 7 21
## 3700 1.161380e-06 0.9999999 8 29
## FDR
## 1917 1.471307e-07
## 1913 1.332424e-06
## 1912 1.332424e-06
## 3702 1.174903e-05
## 2380 3.335146e-05
## 3201 5.297759e-05
## 1372 5.297759e-05
## 1456 8.203918e-05
## 3202 1.994725e-04
## 3700 4.746562e-04
##
## [1] "set_31"
## [1] "Z97634.3" "RASGRP2" "TCF7" "MAN1C1"
## [5] "ACVR2A" "CCR7" "C1orf162" "PLAC8"
## [9] "LDLRAP1" "PLXDC1" "TMEM150A" "CD248"
## [13] "YPEL2" "TRABD2A" "MIR4461" "CTD-3092A11.1"
## [17] "RP11-632K20.7" "LTB" "CHRM3-AS2" "WHAMMP2"
## [21] "RP11-747H7.3" "RP11-1000B6.3" "KCNQ1OT1" "RP1-313I6.12"
## [25] "RP11-434H6.7"
## $immune
## category
## 3016 gse32986 unstim vs gmcsf stim dc up
## 2390 gse26495 naive vs pd1high cd8 tcell up
## 3005 gse32986 gmcsf vs gmcsf and curdlan lowdose stim dc dn
## 1702 gse21670 il6 vs tgfb and il6 treated cd4 tcell up
## 4341 gse4984 lps vs vehicle ctrl treated dc up
## 3596 gse3982 basophil vs cent memory cd4 tcell dn
## 2392 gse26495 naive vs pd1low cd8 tcell up
## 1799 gse22045 treg vs tconv dn
## 4400 gse5542 untreated vs ifna treated epithelial cells 24h dn
## 3391 gse37301 common lymphoid progenitor vs rag2 ko nk cell dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 3016 1.063057e-06 1.0000000 6 25
## 2390 3.744405e-06 0.9999999 6 30
## 3005 4.063936e-06 0.9999998 6 32
## 1702 5.818615e-06 0.9999998 5 22
## 4341 7.492212e-06 0.9999998 5 19
## 3596 1.233604e-05 0.9999998 4 10
## 2392 2.378461e-05 0.9999991 5 24
## 1799 7.385562e-05 0.9999978 4 15
## 4400 7.792784e-05 0.9999976 4 17
## 3391 8.332639e-05 0.9999975 4 15
## FDR
## 3016 0.005420529
## 2390 0.006907337
## 3005 0.006907337
## 1702 0.007417279
## 4341 0.007640557
## 3596 0.010483582
## 2392 0.017325391
## 1799 0.042488128
## 4400 0.042488128
## 3391 0.042488128
##
## [1] "set_37"
## [1] "GCFC2" "OAS1" "GZMB" "ENO3"
## [5] "NCOA7" "GBP1" "MT2A" "RSAD2"
## [9] "SPPL2A" "IRF8" "SFR1" "SLAMF8"
## [13] "AMDHD2" "GNGT2" "KIR3DL1" "ITGAM"
## [17] "NINJ2" "SWI5" "PRF1" "RP11-365H23.1"
## [21] "KIR2DS4" "PTGES3P1" "AKAP2" "KIR2DL3"
## [25] "SERHL2"
## $immune
## category over_represented_pvalue
## 55 gaucher pbmc yf vax stamaril unknown age 7dy up 2.244661e-07
## 45 gaucher pbmc yf vax stamaril unknown age 10dy up 1.517796e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 55 1.000000 9 45 0.001144553
## 45 0.999999 7 39 0.038696207
##
## [1] "set_39"
## [1] "TNFSF10" "PTGER2" "IFI44L" "IFI44" "XCL1"
## [6] "XCL2" "TRPT1" "CX3CR1" "MT1E" "HOPX"
## [11] "RP11-23P13.6" "ZNF683" "NAP1L4P1" "MTHFD2P7" "EEF1GP1"
## [16] "C10orf128" "TRBV20-1" "RP5-1053E7.3" "RP1-182O16.1" "RNU2-2P"
## [21] "TSEN15P1" "SNRPEP4" "MIR155HG" "RNU1-125P" "AL358333.1"
## $reactome
## category over_represented_pvalue
## 127 class a 1 rhodopsin like receptors 1.176486e-05
## 349 gpcr ligand binding 2.673622e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 127 0.9999999 4 19 0.01202368
## 349 0.9999996 4 23 0.01366221
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8958520 478.5 17165476 916.8 NA 17165476 916.8
## Vcells 19169159 146.3 59533611 454.3 65536 78485130 598.8
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0
## [2] GenomicFeatures_1.50.4
## [3] GenomicRanges_1.50.2
## [4] GenomeInfoDb_1.34.9
## [5] org.Hs.eg.db_3.16.0
## [6] AnnotationDbi_1.60.2
## [7] IRanges_2.32.0
## [8] S4Vectors_0.36.2
## [9] Biobase_2.58.0
## [10] BiocGenerics_0.44.0
## [11] goseq_1.50.0
## [12] geneLenDataBase_1.34.0
## [13] BiasedUrn_2.0.10
## [14] fgsea_1.24.0
## [15] biomaRt_2.54.1
## [16] limma_3.54.2
## [17] tidyr_1.3.0
## [18] ggpubr_0.6.0
## [19] ggplot2_3.4.2
## [20] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 tools_4.2.3
## [9] backports_1.4.1 bslib_0.4.2
## [11] utf8_1.2.3 R6_2.5.1
## [13] mgcv_1.8-42 DBI_1.1.3
## [15] colorspace_2.1-0 withr_2.5.0
## [17] tidyselect_1.2.0 prettyunits_1.1.1
## [19] bit_4.0.5 curl_5.0.1
## [21] compiler_4.2.3 cli_3.6.1
## [23] xml2_1.3.4 DelayedArray_0.24.0
## [25] rtracklayer_1.58.0 sass_0.4.5
## [27] scales_1.2.1 rappdirs_0.3.3
## [29] Rsamtools_2.14.0 stringr_1.5.0
## [31] digest_0.6.31 rmarkdown_2.21
## [33] XVector_0.38.0 pkgconfig_2.0.3
## [35] htmltools_0.5.5 MatrixGenerics_1.10.0
## [37] dbplyr_2.3.2 fastmap_1.1.1
## [39] rlang_1.1.0 rstudioapi_0.14
## [41] RSQLite_2.3.1 BiocIO_1.8.0
## [43] jquerylib_0.1.4 generics_0.1.3
## [45] jsonlite_1.8.4 BiocParallel_1.32.6
## [47] dplyr_1.1.2 car_3.1-2
## [49] RCurl_1.98-1.12 magrittr_2.0.3
## [51] GO.db_3.16.0 GenomeInfoDbData_1.2.9
## [53] Matrix_1.6-4 Rcpp_1.0.10
## [55] munsell_0.5.0 fansi_1.0.4
## [57] abind_1.4-5 lifecycle_1.0.3
## [59] stringi_1.7.12 yaml_2.3.7
## [61] carData_3.0-5 SummarizedExperiment_1.28.0
## [63] zlibbioc_1.44.0 BiocFileCache_2.6.1
## [65] grid_4.2.3 blob_1.2.4
## [67] parallel_4.2.3 crayon_1.5.2
## [69] lattice_0.20-45 splines_4.2.3
## [71] Biostrings_2.66.0 cowplot_1.1.1
## [73] hms_1.1.3 KEGGREST_1.38.0
## [75] knitr_1.44 pillar_1.9.0
## [77] rjson_0.2.21 ggsignif_0.6.4
## [79] codetools_0.2-19 fastmatch_1.1-3
## [81] XML_3.99-0.14 glue_1.6.2
## [83] evaluate_0.20 png_0.1-8
## [85] vctrs_0.6.2 gtable_0.3.3
## [87] purrr_1.0.1 cachem_1.0.7
## [89] xfun_0.39 broom_1.0.4
## [91] restfulr_0.0.15 rstatix_0.7.2
## [93] tibble_3.2.1 GenomicAlignments_1.34.1
## [95] memoise_2.0.1